data_4X1K # _model_server_result.job_id B8RmSJuqrFp30RgcDX4_AQ _model_server_result.datetime_utc '2024-11-27 02:02:31' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4x1k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 4X1K # _exptl.entry_id 4X1K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4X1K _cell.length_a 66.73 _cell.length_b 128.3 _cell.length_c 254.38 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X1K _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H N N ? 6 M N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 F O2G GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc2 F O2B GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc3 K O2G GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc4 K O2B GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B GDP doub 195 n n PB O2B GDP sing 196 n n PB O3B GDP sing 197 n n PB O3A GDP sing 198 n n O2B HOB2 GDP sing 199 n n O3B HOB3 GDP sing 200 n n O3A PA GDP sing 201 n n PA O1A GDP doub 202 n n PA O2A GDP sing 203 n n PA O5' GDP sing 204 n n O2A HOA2 GDP sing 205 n n O5' C5' GDP sing 206 n n C5' C4' GDP sing 207 n n C5' H5' GDP sing 208 n n C5' "H5''" GDP sing 209 n n C4' O4' GDP sing 210 n n C4' C3' GDP sing 211 n n C4' H4' GDP sing 212 n n O4' C1' GDP sing 213 n n C3' O3' GDP sing 214 n n C3' C2' GDP sing 215 n n C3' H3' GDP sing 216 n n O3' HO3' GDP sing 217 n n C2' O2' GDP sing 218 n n C2' C1' GDP sing 219 n n C2' H2' GDP sing 220 n n O2' HO2' GDP sing 221 n n C1' N9 GDP sing 222 n n C1' H1' GDP sing 223 n n N9 C8 GDP sing 224 n y N9 C4 GDP sing 225 n y C8 N7 GDP doub 226 n y C8 H8 GDP sing 227 n n N7 C5 GDP sing 228 n y C5 C6 GDP sing 229 n n C5 C4 GDP doub 230 n y C6 O6 GDP doub 231 n n C6 N1 GDP sing 232 n n N1 C2 GDP sing 233 n n N1 HN1 GDP sing 234 n n C2 N2 GDP sing 235 n n C2 N3 GDP doub 236 n n N2 HN21 GDP sing 237 n n N2 HN22 GDP sing 238 n n N3 C4 GDP sing 239 n n # _atom_sites.entry_id 4X1K _atom_sites.fract_transf_matrix[1][1] 0.014999 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007805 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.003931 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code F 4 GTP A 1 600 600 GTP GTP . G 5 MG A 1 601 601 MG MG . H 6 GDP B 1 501 600 GDP GDP . I 7 LOC B 1 502 601 LOC 618 . J 8 3WZ B 1 503 1 3WZ PFE . K 4 GTP C 1 600 600 GTP GTP . L 5 MG C 1 601 601 MG MG . M 6 GDP D 1 501 600 GDP GDP . N 7 LOC D 1 502 601 LOC 618 . O 8 3WZ D 1 503 1 3WZ PFE . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB GDP . . . H 6 -1.689 85.54 92.559 1 126.01 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . H 6 -0.843 86.526 91.79 1 126.04 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . H 6 -1.613 84.098 92.004 1 123.35 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . H 6 -3.083 86.176 92.54 1 122.8 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . H 6 -1.118 85.502 94.045 1 131.94 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . H 6 0.111 84.892 94.849 1 134.22 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . H 6 1.048 84.161 93.898 1 136.75 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . H 6 0.857 85.972 95.532 1 135.21 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . H 6 -0.544 83.922 95.921 1 132.84 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . H 6 -0.34 84.029 97.347 1 135.12 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . H 6 0.52 82.88 97.818 1 137.83 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . H 6 1.703 82.817 96.994 1 138.22 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . H 6 0.998 82.938 99.276 1 139.73 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . H 6 0.83 81.708 99.981 1 139.93 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . H 6 2.469 83.362 99.158 1 139.47 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . H 6 3.244 82.846 100.24 1 136.81 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . H 6 2.853 82.746 97.81 1 139.36 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . H 6 3.96 83.393 97.091 1 137.79 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . H 6 3.934 84.599 96.44 1 136.57 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . H 6 4.962 84.788 95.647 1 138.64 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . H 6 5.726 83.638 95.797 1 140.86 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . H 6 6.987 83.183 95.154 1 141.98 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . H 6 7.599 83.719 94.223 1 143.71 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . H 6 7.41 81.961 95.655 1 138.32 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . H 6 6.755 81.221 96.606 1 134.95 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . H 6 7.331 80.085 96.984 1 132.71 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . H 6 5.599 81.586 97.164 1 136.33 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . H 6 5.138 82.785 96.715 1 138.62 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #